Merge pull request #290 from huerqiang/master

Change the download method for KEGG data

DESCRIPTION

@@ -2,7 +2,7 @@ Package: clusterProfiler
 Type: Package
 Title: statistical analysis and visualization of functional profiles for
     genes and gene clusters
-Version: 3.17.1
+Version: 3.17.2
 Authors@R: c(
     person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role  = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
     person(given = "Li-Gen",      family = "Wang",      email = "[email protected]",   role  = "ctb"),

R/enricher.R

@@ -3,7 +3,7 @@
 ##'
 ##' @title enricher
 ##' @param gene a vector of gene id
-##' @param pvalueCutoff pvalue cutoff on enrichment tests to report
+##' @param pvalueCutoff adjusted pvalue cutoff on enrichment tests to report
 ##' @param pAdjustMethod  one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
 ##' @param universe background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background.
 ##' @param minGSSize minimal size of genes annotated for testing
@@ -44,7 +44,7 @@ enricher <- function(gene,
 ##' @param minGSSize minimal size of each geneSet for analyzing
 ##' @param maxGSSize maximal size of genes annotated for testing
 ##' @param eps This parameter sets the boundary for calculating the p value.
-##' @param pvalueCutoff pvalue cutoff
+##' @param pvalueCutoff adjusted pvalue cutoff
 ##' @param pAdjustMethod p value adjustment method
 ##' @param TERM2GENE user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
 ##' @param TERM2NAME user input of TERM TO NAME mapping, a data.frame of 2 column with term and name

R/kegg-utilities.R

@@ -92,8 +92,15 @@ kegg_rest <- function(rest_url) {
 
     message("Reading KEGG annotation online:\n" )
     f <- tempfile()
-    dl <- tryCatch(downloader::download(rest_url, destfile = f, quiet = TRUE),
+    ## dl <- tryCatch(downloader::download(rest_url, destfile = f, quiet = TRUE),
+    if (capabilities("libcurl")) {
+        dl <- tryCatch(utils::download.file(rest_url, destfile = f, quiet = TRUE, method = "libcurl"),
                    error = function(e) NULL)
+    } else {
+        dl <- tryCatch(downloader::download(rest_url, destfile = f, quiet = TRUE),
+                   error = function(e) NULL)
+    }
+
     if (is.null(dl)) {
         message("fail to download KEGG data...")
         return(NULL)